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==Data from publications== | ==Data from publications== | ||
- | The following is a list of data sets with associated PubMed IDs that have supplied data to the GPMDB Project through the data sources mentioned above. The list was current, as of February | + | The following is a list of data sets with associated PubMed IDs that have supplied data to the GPMDB Project through the data sources mentioned above. The list was current, as of February 9, 2020. |
#Lipton MS, Pasa-Tolic' L, Anderson GA, Anderson DJ, Auberry DL, Battista JR, Daly MJ, Fredrickson J, Hixson KK, Kostandarithes H, Masselon C, Markillie LM, Moore RJ, Romine MF, Shen Y, Stritmatter E, Tolic' N, Udseth HR, Venkateswaran A, Wong KK, Zhao R, Smith RD, (2002) "Global analysis of the Deinococcus radiodurans proteome by using accurate mass tags." <i>Proc Natl Acad Sci U S A</i> <b>99</b>(17):11049–54; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/12177431 12177431]; doi: [https://dx.doi.org/10.1073/pnas.172170199 10.1073/pnas.172170199]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/12177431 498]. | #Lipton MS, Pasa-Tolic' L, Anderson GA, Anderson DJ, Auberry DL, Battista JR, Daly MJ, Fredrickson J, Hixson KK, Kostandarithes H, Masselon C, Markillie LM, Moore RJ, Romine MF, Shen Y, Stritmatter E, Tolic' N, Udseth HR, Venkateswaran A, Wong KK, Zhao R, Smith RD, (2002) "Global analysis of the Deinococcus radiodurans proteome by using accurate mass tags." <i>Proc Natl Acad Sci U S A</i> <b>99</b>(17):11049–54; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/12177431 12177431]; doi: [https://dx.doi.org/10.1073/pnas.172170199 10.1073/pnas.172170199]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/12177431 498]. | ||
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#Arima N, Sasaki Y, Lee LH, Zhang H, Figueiredo JL, Mlynarchik AK, Qiao J, Yamada I, Higashi H, Ha AH, Halu A, Mizuno K, Singh SA, Yamazaki Y, Aikawa M, (2020) "Multiorgan Systems Study Reveals Igfbp7 as a Suppressor of Gluconeogenesis after Gastric Bypass Surgery." <i>J Proteome Res</i> <b>19</b>(1):129–143; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31661273 31661273]; doi: [https://dx.doi.org/10.1021/acs.jproteome.9b00441 10.1021/acs.jproteome.9b00441]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31661273 4]. | #Arima N, Sasaki Y, Lee LH, Zhang H, Figueiredo JL, Mlynarchik AK, Qiao J, Yamada I, Higashi H, Ha AH, Halu A, Mizuno K, Singh SA, Yamazaki Y, Aikawa M, (2020) "Multiorgan Systems Study Reveals Igfbp7 as a Suppressor of Gluconeogenesis after Gastric Bypass Surgery." <i>J Proteome Res</i> <b>19</b>(1):129–143; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31661273 31661273]; doi: [https://dx.doi.org/10.1021/acs.jproteome.9b00441 10.1021/acs.jproteome.9b00441]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31661273 4]. | ||
#Mallam AL, Sae-Lee W, Schaub JM, Tu F, Battenhouse A, Jang YJ, Kim J, Wallingford JB, Finkelstein IJ, Marcotte EM, Drew K, (2019) "Systematic Discovery of Endogenous Human Ribonucleoprotein Complexes." <i>Cell Rep</i> <b>29</b>(5):1351–1368.e5; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31665645 31665645]; doi: [https://dx.doi.org/10.1016/j.celrep.2019.09.060 10.1016/j.celrep.2019.09.060]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31665645 122]. | #Mallam AL, Sae-Lee W, Schaub JM, Tu F, Battenhouse A, Jang YJ, Kim J, Wallingford JB, Finkelstein IJ, Marcotte EM, Drew K, (2019) "Systematic Discovery of Endogenous Human Ribonucleoprotein Complexes." <i>Cell Rep</i> <b>29</b>(5):1351–1368.e5; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31665645 31665645]; doi: [https://dx.doi.org/10.1016/j.celrep.2019.09.060 10.1016/j.celrep.2019.09.060]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31665645 122]. | ||
- | #Sohier P, Sanson R, Leduc M, Audebourg A, Broussard C, Salnot V, Just PA, Pasmant E, Mayeux P, Guillonneau F, Romagnolo B, Perret C, Terris B, (2019) "Proteome analysis of formalin-fixed paraffin-embedded colorectal adenomas reveals the heterogeneous nature of traditional serrated adenomas compared to other colorectal adenomas." <i>J Pathol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31729028 31729028]; doi: [https://dx.doi.org/10.1002/path.5366 10.1002/path.5366]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31729028 | + | #Sohier P, Sanson R, Leduc M, Audebourg A, Broussard C, Salnot V, Just PA, Pasmant E, Mayeux P, Guillonneau F, Romagnolo B, Perret C, Terris B, (2019) "Proteome analysis of formalin-fixed paraffin-embedded colorectal adenomas reveals the heterogeneous nature of traditional serrated adenomas compared to other colorectal adenomas." <i>J Pathol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31729028 31729028]; doi: [https://dx.doi.org/10.1002/path.5366 10.1002/path.5366]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31729028 55]. |
#Newey A, Griffiths B, Michaux J, Pak HS, Stevenson BJ, Woolston A, Semiannikova M, Spain G, Barber LJ, Matthews N, Rao S, Watkins D, Chau I, Coukos G, Racle J, Gfeller D, Starling N, Cunningham D, Bassani-Sternberg M, Gerlinger M, (2019) "Immunopeptidomics of colorectal cancer organoids reveals a sparse HLA class I neoantigen landscape and no increase in neoantigens with interferon or MEK-inhibitor treatment." <i>J Immunother Cancer</i> <b>7</b>(1):309; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31735170 31735170]; doi: [https://dx.doi.org/10.1186/s40425-019-0769-8 10.1186/s40425-019-0769-8]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31735170 193]. | #Newey A, Griffiths B, Michaux J, Pak HS, Stevenson BJ, Woolston A, Semiannikova M, Spain G, Barber LJ, Matthews N, Rao S, Watkins D, Chau I, Coukos G, Racle J, Gfeller D, Starling N, Cunningham D, Bassani-Sternberg M, Gerlinger M, (2019) "Immunopeptidomics of colorectal cancer organoids reveals a sparse HLA class I neoantigen landscape and no increase in neoantigens with interferon or MEK-inhibitor treatment." <i>J Immunother Cancer</i> <b>7</b>(1):309; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31735170 31735170]; doi: [https://dx.doi.org/10.1186/s40425-019-0769-8 10.1186/s40425-019-0769-8]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31735170 193]. | ||
#Thompson A, Wölmer N, Koncarevic S, Selzer S, Böhm G, Legner H, Schmid P, Kienle S, Penning P, Höhle C, Berfelde A, Martinez-Pinna R, Farztdinov V, Jung S, Kuhn K, Pike I, (2019) "TMTpro: Design, Synthesis, and Initial Evaluation of a Proline-Based Isobaric 16-Plex Tandem Mass Tag Reagent Set." <i>Anal Chem</i> <b>91</b>(24):15941–15950; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31738517 31738517]; doi: [https://dx.doi.org/10.1021/acs.analchem.9b04474 10.1021/acs.analchem.9b04474]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31738517 20]. | #Thompson A, Wölmer N, Koncarevic S, Selzer S, Böhm G, Legner H, Schmid P, Kienle S, Penning P, Höhle C, Berfelde A, Martinez-Pinna R, Farztdinov V, Jung S, Kuhn K, Pike I, (2019) "TMTpro: Design, Synthesis, and Initial Evaluation of a Proline-Based Isobaric 16-Plex Tandem Mass Tag Reagent Set." <i>Anal Chem</i> <b>91</b>(24):15941–15950; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31738517 31738517]; doi: [https://dx.doi.org/10.1021/acs.analchem.9b04474 10.1021/acs.analchem.9b04474]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31738517 20]. | ||
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#Nobre LV, Nightingale K, Ravenhill BJ, Antrobus R, Soday L, Nichols J, Davies JA, Seirafian S, Wang EC, Davison AJ, Wilkinson GW, Stanton RJ, Huttlin EL, Weekes MP, (2019) "Human cytomegalovirus interactome analysis identifies degradation hubs, domain associations and viral protein functions." <i>Elife</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31873071 31873071]; doi: [https://dx.doi.org/10.7554/eLife.49894 10.7554/eLife.49894]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31873071 354]. | #Nobre LV, Nightingale K, Ravenhill BJ, Antrobus R, Soday L, Nichols J, Davies JA, Seirafian S, Wang EC, Davison AJ, Wilkinson GW, Stanton RJ, Huttlin EL, Weekes MP, (2019) "Human cytomegalovirus interactome analysis identifies degradation hubs, domain associations and viral protein functions." <i>Elife</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31873071 31873071]; doi: [https://dx.doi.org/10.7554/eLife.49894 10.7554/eLife.49894]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31873071 354]. | ||
#Mühlhofer M, Berchtold E, Stratil CG, Csaba G, Kunold E, Bach NC, Sieber SA, Haslbeck M, Zimmer R, Buchner J, (2019) "The Heat Shock Response in Yeast Maintains Protein Homeostasis by Chaperoning and Replenishing Proteins." <i>Cell Rep</i> <b>29</b>(13):4593–4607.e8; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31875563 31875563]; doi: [https://dx.doi.org/10.1016/j.celrep.2019.11.109 10.1016/j.celrep.2019.11.109]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31875563 15]. | #Mühlhofer M, Berchtold E, Stratil CG, Csaba G, Kunold E, Bach NC, Sieber SA, Haslbeck M, Zimmer R, Buchner J, (2019) "The Heat Shock Response in Yeast Maintains Protein Homeostasis by Chaperoning and Replenishing Proteins." <i>Cell Rep</i> <b>29</b>(13):4593–4607.e8; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31875563 31875563]; doi: [https://dx.doi.org/10.1016/j.celrep.2019.11.109 10.1016/j.celrep.2019.11.109]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31875563 15]. | ||
- | #Van JAD, Clotet-Freixas S, Zhou J, Batruch I, Sun C, Glogauer M, Rampoldi L, Elia Y, Mahmud F, Sochett E, Diamandis EP, Scholey J, Konvalinka A, (2019) "Peptidomic analysis of urine from youths with early type 1 diabetes reveals novel bioactivity of uromodulin peptides <i>in vitro</i>." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31879271 31879271]; doi: [https://dx.doi.org/10.1074/mcp.RA119.001858 10.1074/mcp.RA119.001858]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31879271 | + | #Van JAD, Clotet-Freixas S, Zhou J, Batruch I, Sun C, Glogauer M, Rampoldi L, Elia Y, Mahmud F, Sochett E, Diamandis EP, Scholey J, Konvalinka A, (2019) "Peptidomic analysis of urine from youths with early type 1 diabetes reveals novel bioactivity of uromodulin peptides <i>in vitro</i>." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31879271 31879271]; doi: [https://dx.doi.org/10.1074/mcp.RA119.001858 10.1074/mcp.RA119.001858]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31879271 90]. |
#Nguyen AM, Zhou J, Sicairos B, Sonney S, Du Y, (2019) "Upregulation of CD73 Confers Acquired Radioresistance and is Required for Maintaining Irradiation-Selected Pancreatic Cancer Cells in a Mesenchymal State." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31879272 31879272]; doi: [https://dx.doi.org/10.1074/mcp.RA119.001779 10.1074/mcp.RA119.001779]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31879272 20]. | #Nguyen AM, Zhou J, Sicairos B, Sonney S, Du Y, (2019) "Upregulation of CD73 Confers Acquired Radioresistance and is Required for Maintaining Irradiation-Selected Pancreatic Cancer Cells in a Mesenchymal State." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31879272 31879272]; doi: [https://dx.doi.org/10.1074/mcp.RA119.001779 10.1074/mcp.RA119.001779]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31879272 20]. | ||
#Mugahid DA, Sengul TG, You X, Wang Y, Steil L, Bergmann N, Radke MH, Ofenbauer A, Gesell-Salazar M, Balogh A, Kempa S, Tursun B, Robbins CT, Völker U, Chen W, Nelson L, Gotthardt M, (2019) "Proteomic and Transcriptomic Changes in Hibernating Grizzly Bears Reveal Metabolic and Signaling Pathways that Protect against Muscle Atrophy." <i>Sci Rep</i> <b>9</b>(1):19976; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31882638 31882638]; doi: [https://dx.doi.org/10.1038/s41598-019-56007-8 10.1038/s41598-019-56007-8]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31882638 16]. | #Mugahid DA, Sengul TG, You X, Wang Y, Steil L, Bergmann N, Radke MH, Ofenbauer A, Gesell-Salazar M, Balogh A, Kempa S, Tursun B, Robbins CT, Völker U, Chen W, Nelson L, Gotthardt M, (2019) "Proteomic and Transcriptomic Changes in Hibernating Grizzly Bears Reveal Metabolic and Signaling Pathways that Protect against Muscle Atrophy." <i>Sci Rep</i> <b>9</b>(1):19976; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31882638 31882638]; doi: [https://dx.doi.org/10.1038/s41598-019-56007-8 10.1038/s41598-019-56007-8]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31882638 16]. | ||
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#Hose J, Escalante LE, Clowers KJ, Dutcher HA, Robinson D, Bouriakov V, Coon JJ, Shishkova E, Gasch AP, (2020) "The genetic basis of aneuploidy tolerance in wild yeast." <i>Elife</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31909711 31909711]; doi: [https://dx.doi.org/10.7554/eLife.52063 10.7554/eLife.52063]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31909711 24]. | #Hose J, Escalante LE, Clowers KJ, Dutcher HA, Robinson D, Bouriakov V, Coon JJ, Shishkova E, Gasch AP, (2020) "The genetic basis of aneuploidy tolerance in wild yeast." <i>Elife</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31909711 31909711]; doi: [https://dx.doi.org/10.7554/eLife.52063 10.7554/eLife.52063]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31909711 24]. | ||
#Bian Y, Zheng R, Bayer FP, Wong C, Chang YC, Meng C, Zolg DP, Reinecke M, Zecha J, Wiechmann S, Heinzlmeir S, Scherr J, Hemmer B, Baynham M, Gingras AC, Boychenko O, Kuster B, (2020) "Robust, reproducible and quantitative analysis of thousands of proteomes by micro-flow LC-MS/MS." <i>Nat Commun</i> <b>11</b>(1):157; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31919466 31919466]; doi: [https://dx.doi.org/10.1038/s41467-019-13973-x 10.1038/s41467-019-13973-x]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31919466 2175]. | #Bian Y, Zheng R, Bayer FP, Wong C, Chang YC, Meng C, Zolg DP, Reinecke M, Zecha J, Wiechmann S, Heinzlmeir S, Scherr J, Hemmer B, Baynham M, Gingras AC, Boychenko O, Kuster B, (2020) "Robust, reproducible and quantitative analysis of thousands of proteomes by micro-flow LC-MS/MS." <i>Nat Commun</i> <b>11</b>(1):157; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31919466 31919466]; doi: [https://dx.doi.org/10.1038/s41467-019-13973-x 10.1038/s41467-019-13973-x]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31919466 2175]. | ||
+ | #Meng K, Lu S, Yan X, Sun Y, Gao J, Wang Y, Yin X, Sun Z, He QY, (2020) "Quantitative Mitochondrial Proteomics Reveals ANXA7 as a Crucial Factor in Mitophagy." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31975592 31975592]; doi: [https://dx.doi.org/10.1021/acs.jproteome.9b00800 10.1021/acs.jproteome.9b00800]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31975592 3]. | ||
+ | #Gonnet J, Poncelet L, Meriaux C, Gonçalves E, Weiss L, Tchitchek N, Pedruzzi E, Soria A, Boccara D, Vogt A, Bonduelle O, Hamm G, Ait-Belkacem R, Stauber J, Fournier I, Wisztorski M, Combadiere B, (2020) "Mechanisms of innate events during skin reaction following intradermal injection of seasonal influenza vaccine." <i>J Proteomics</i> <b>216</b>:103670; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31991189 31991189]; doi: [https://dx.doi.org/10.1016/j.jprot.2020.103670 10.1016/j.jprot.2020.103670]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31991189 48]. |
GPMDB was originally constructed to serve as a reference work for all publicly available proteomics generated using tandem mass spectrometry. Public data is downloaded and reanalyzed using the current version of X! Tandem. The result files generated by the reanalysis and the relevant metadata are imported into the database and made available through the associated web site, ftp site and REST interfaces.
Contents |
The following public data repositories are checked daily for new suitable raw data for reanalysis:
Data made available from specific large projects, such as CPTAC or the Human Proteome Atlas, are also included when they are made available. Every effort is made so that reanalyzed results from all data sources are made available within 48 hours of their being released. In addition, data from lab web sites, ftp sites and direct contributions through the GPM sites made available to researchers are imported into GPMDB as part of a daily incremental update process.
GPMDB has been in operation since Jan. 1, 2004. Several large data source repositories have come into existence and ceased activity in the period since that time. All of the data from those repositories (e.g., TRANCHE, Peptidome) were reanalyzed and stored in GPMDB and they are still available even though the source repository sites are no longer active.
Simply because data is made available does not mean that it will be included in GPMDB. The data must be approved our quality control AI for its initial acceptance and it may be rejected subsequently because of either quality or originality concerns.
CAUTION: Many papers contain serious errors in their Methods sections. When using data from the literature, it is important to be skeptical of any experimental parameter (cell line, tissue type, modification reagents, quantitation methoods, etc.) that may impact on your use of the data. We have tried to correct any obvious errors, but there is no way to guarantee that we found them all. When attempting to analyze or reproduce results, keep in mind the likelyhood that even key parts of the experiment methods may have been recorded incorrectly in the associated manuscript, as methods are rarely reviewed properly in the current journal publication process.
The following is a list of data sets with associated PubMed IDs that have supplied data to the GPMDB Project through the data sources mentioned above. The list was current, as of February 9, 2020.